Wolverine travels back in time to stop Mystique from assassinating Bolivar Trask, whose death leads to the creation of the Sentinels, which are robots designed to kill mutants.

The all-powerful mutant Apocalypse, who is long revered as a god, wants to cause extinction on earth. The X-Men must work together to demolish his plans.

After a mishap, Jean Grey is struck by a powerful ray of energy which she absorbs into her body, turning her into an uncontrollable liability for the X-Men.

During the Cold War, fellow mutants Charles Xavier and Erik Lehnsherr join forces with other mutants to save humanity from a nuclear attack and a possible world war.